This study provides a metataxonomic analysis of the fungal communities in soils under slash‐and‐burn agroforestry system and offers new insights into the relationships between fungal populations and soil physicochemical features such as pH, the particle size distribution, easily oxidizable organic carbon, total nitrogen, available phosphorus, and the mineralogical composition. Soils from three locations in central Mozambique—Vanduzi, Sussundenga, and Macate—that are subjected to slash‐and‐burn were considered to assess the effects of the forest fallow length (temporal variation) and of the land use (charcoal kiln, crop field, and forest; meaning horizontal variation) on the fungal community. The fungi of the genetic horizons (vertical variation) were also considered. Most of the detected fungi were decomposers, antagonists of plant pathogens, and plant‐growth promoters; they were differently distributed in relation to the soil's physicochemical properties and the soil use. The variations in the fungi distribution among the locations and between the horizons were considerable, while there were few variations between the different land‐use types. The limited differences between land uses indicate the inability of a forest fallow period shorter than 50 years to improve soil fertility and induce changes in the fungal community. The pedological approach used to identify and sample soil horizons allowed us to clearly distinguish the fungal community of the A horizons, those richest in organics and nutrients, and that of the Bo horizons, which have poor fertility.